Contacts of the helix formed by residues 442 - 451 (chain A) in PDB entry 4I1R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 442 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A SER* 3.0 36.7 + - - +
425A MET* 4.0 14.6 - - + -
440A LEU 3.2 0.6 + - - -
441A CYS* 1.4 69.0 - - - +
443A GLN* 1.3 53.0 + - - +
445A ILE* 3.1 13.0 + - - +
446A LEU* 2.9 40.9 + - + +
459A PHE* 3.7 10.5 - - + -
461A LEU* 3.7 17.3 - - + -
463A MET* 4.0 11.4 - - + -
488A PHE* 3.6 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A GLY 3.7 12.2 + - - +
422A ASN* 3.2 23.5 + - - +
423A SER* 2.9 48.1 + - - +
441A CYS* 3.3 11.4 - - - -
442A VAL* 1.3 76.7 - - - +
444A ASN* 1.3 58.9 + - - +
446A LEU* 3.2 16.3 - - + +
447A LYS* 2.9 38.2 + - - +
488A PHE* 6.0 1.6 - - - -
551A ARG* 5.6 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A CYS* 3.1 36.0 + - - +
443A GLN* 1.3 76.7 - - - +
445A ILE* 1.4 57.8 + - + +
447A LYS* 2.9 37.8 + - - +
448A LEU* 3.0 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A VAL* 4.0 27.6 - - + -
399A LEU* 4.7 3.0 - - + +
410A LEU* 4.1 1.6 - - + -
425A MET* 3.8 29.2 - - + -
440A LEU* 4.3 13.9 - - + +
441A CYS 3.4 19.7 - - - +
442A VAL* 3.1 16.7 + - - +
444A ASN* 1.4 72.8 - - + +
446A LEU* 1.3 51.7 + - - +
448A LEU* 3.3 15.3 + - + +
449A MET* 2.9 53.6 + - + +
459A PHE* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A VAL* 2.9 35.6 + - + +
443A GLN* 3.2 21.3 - - + +
445A ILE* 1.3 73.8 - - - +
447A LYS* 1.4 53.0 + - + +
449A MET* 3.0 11.8 + - - +
450A GLN* 2.9 48.4 + - - +
459A PHE* 3.4 28.3 - - + -
486A ILE* 4.3 17.2 - - + +
488A PHE* 4.1 22.4 - - + -
551A ARG* 5.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLN* 2.9 23.2 + - - +
444A ASN* 2.9 29.6 + - - +
446A LEU* 1.4 70.8 - - + +
448A LEU* 1.3 61.1 + - + +
450A GLN* 3.6 24.0 + - - +
451A GLU* 3.6 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP* 5.6 4.0 - - - +
399A LEU* 4.3 25.6 - - + -
444A ASN* 3.0 31.5 + - + +
445A ILE* 3.5 12.3 - - + +
447A LYS* 1.3 74.0 - - + +
449A MET* 1.3 65.7 + - - +
451A GLU* 3.3 33.0 + - - +
452A LYS* 3.7 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A PHE* 4.3 7.0 - - + -
399A LEU* 3.8 15.3 - - + -
402A LEU* 4.4 1.6 - - + -
410A LEU* 3.7 35.9 - - + -
445A ILE* 2.9 26.6 + - + +
446A LEU* 3.4 12.8 - - - +
448A LEU* 1.3 75.0 - - - +
450A GLN* 1.3 60.5 + - - +
452A LYS* 3.1 27.1 + - - +
454A THR* 5.2 0.3 + - - -
457A ASN* 3.1 37.9 - - - +
458A VAL 5.3 0.2 - - - +
459A PHE* 3.7 26.5 - - + -
484A ALA* 3.5 8.8 - - - +
486A ILE* 3.6 13.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LEU* 2.9 27.9 + - - +
447A LYS* 3.7 20.6 - - - +
448A LEU 3.2 0.4 - - - -
449A MET* 1.3 71.9 - - - +
451A GLU* 1.3 56.2 + - + +
452A LYS 3.0 16.7 + - - +
484A ALA* 3.9 8.4 + - - +
486A ILE* 3.7 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LYS 3.6 15.3 - - - +
448A LEU* 3.4 25.0 - - - +
449A MET 3.2 0.8 - - - -
450A GLN* 1.3 72.8 - - + +
452A LYS* 1.3 66.3 + - + +
453A GLU* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il